[English] 日本語
Yorodumi
- PDB-5yiw: Caulobacter crescentus GcrA DNA-binding domain (DBD) in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yiw
TitleCaulobacter crescentus GcrA DNA-binding domain (DBD) in complex with methylated dsDNA (crystal form 2)
Components
  • Cell cycle regulatory protein GcrA
  • DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / Caulobacter crescentus / GcrA / DNA-binding / transcription factor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyGcrA cell cycle regulator / GcrA cell cycle regulator / metal ion binding / (R,R)-2,3-BUTANEDIOL / DNA / DNA (> 10) / Cell cycle regulatory protein GcrA
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsWu, X. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670067 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.
Authors: Wu, X. / Haakonsen, D.L. / Sanderlin, A.G. / Liu, Y.J. / Shen, L. / Zhuang, N. / Laub, M.T. / Zhang, Y.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell cycle regulatory protein GcrA
B: Cell cycle regulatory protein GcrA
C: Cell cycle regulatory protein GcrA
D: DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7386
Polymers22,6485
Non-polymers901
Water2,144119
1
A: Cell cycle regulatory protein GcrA
D: DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1044
Polymers12,0143
Non-polymers901
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-4 kcal/mol
Surface area5500 Å2
MethodPISA
2
B: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3060 Å2
MethodPISA
3
C: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 63.658, 126.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein/peptide Cell cycle regulatory protein GcrA


Mass: 5317.199 Da / Num. of mol.: 3 / Fragment: DNA-binding domain (DBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: gcrA, CCNA_02328 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3C9J4
#2: DNA chain DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')


Mass: 3299.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')


Mass: 3397.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.05M Potassium phosphate monobasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 29530 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Rsym value: 0.07 / Χ2: 0.95 / Net I/σ(I): 22.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1394 / CC1/2: 0.88 / Rpim(I) all: 0.3 / Rrim(I) all: 0.8 / Rsym value: 0.74 / Χ2: 0.95 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIU

5yiu


Resolution: 1.551→28.745 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.234 1472 5 %
Rwork0.2036 --
obs0.2052 29459 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 1.551→28.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 434 0 119 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061527
X-RAY DIFFRACTIONf_angle_d1.0082148
X-RAY DIFFRACTIONf_dihedral_angle_d20.786569
X-RAY DIFFRACTIONf_chiral_restr0.037253
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5507-1.60070.32941260.26952488X-RAY DIFFRACTION99
1.6007-1.6580.27921310.24142510X-RAY DIFFRACTION100
1.658-1.72430.28751220.21662508X-RAY DIFFRACTION99
1.7243-1.80280.22231390.20432524X-RAY DIFFRACTION100
1.8028-1.89780.26191330.20872537X-RAY DIFFRACTION100
1.8978-2.01670.23731270.21432575X-RAY DIFFRACTION100
2.0167-2.17240.27061280.20172520X-RAY DIFFRACTION100
2.1724-2.39090.21521430.20392568X-RAY DIFFRACTION100
2.3909-2.73660.23271370.22322562X-RAY DIFFRACTION100
2.7366-3.44690.2511320.21532570X-RAY DIFFRACTION99
3.4469-28.75040.20811540.17842625X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more